Check Code/Documentation Consistency

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Description

Find inconsistencies between actual and documented ‘structure’
of R objects in a package. codoc compares names and
optionally also corresponding positions and default values of the
arguments of functions. codocClasses and codocData
compare slot names of S4 classes and variable names of data sets,
respectively.

Usage

Arguments

package

a character string naming an installed package.

dir

a character string specifying the path to a package's root
source directory. This must contain the subdirectories ‘man’
with R documentation sources (in Rd format) and ‘R’ with R
code. Only used if package is not given.

lib.loc

a character vector of directory names of R libraries,
or NULL. The default value of NULL corresponds to all
libraries currently known. The specified library trees are used to
search for package.

use.values

if FALSE, do not use function default values
when comparing code and docs. Otherwise, compare all default
values if TRUE, and only the ones documented in the usage
otherwise (default).

verbose

a logical. If TRUE, additional diagnostics are
printed.

Details

The purpose of codoc is to check whether the documented usage
of function objects agrees with their formal arguments as defined in
the R code. This is not always straightforward, in particular as the
usage information for methods to generic functions often employs the
name of the generic rather than the method.

The following algorithm is used. If an installed package is used, it
is loaded (unless it is the base package), after possibly
detaching an already loaded version of the package. Otherwise, if the
sources are used, the R code files of the package are collected and
sourced in a new environment. Then, the usage sections of the Rd
files are extracted and parsed ‘as much as possible’ to give
the formals documented. For interpreted functions in the code
environment, the formals are compared between code and documentation
according to the values of the argument use.values. Synopsis
sections are used if present; their occurrence is reported if
verbose is true.

If a package has a namespace both exported and unexported objects are
checked, as well as registered S3 methods. (In the unlikely event of
differences the order is exported objects in the package, registered
S3 methods and finally objects in the namespace and only the first
found is checked.)

Currently, the R documentation format has no high-level markup for the
basic ‘structure’ of classes and data sets (similar to the usage
sections for function synopses). Variable names for data frames in
documentation objects obtained by suitably editing ‘templates’
created by prompt are recognized by codocData
and used provided that the documentation object is for a single data
frame (i.e., only has one alias). codocClasses analogously
handles slot names for classes in documentation objects obtained by
editing shells created by promptClass.

Help files named ‘pkgname-defunct.Rd’ for the
appropriate pkgname are checked more loosely, as they may
have undocumented arguments.

Value

codoc returns an object of class "codoc". Currently,
this is a list which, for each Rd object in the package where an
inconsistency was found, contains an element with a list of the
mismatches (which in turn are lists with elements code and
docs, giving the corresponding arguments obtained from the
function's code and documented usage).

codocClasses and codocData return objects of class
"codocClasses" and "codocData", respectively, with a
structure similar to class "codoc".

There are print methods for nicely displaying the information
contained in such objects.

Note

The default for use.values has been changed from
FALSE to NULL, for R versions 1.9.0 and later.